CLARA - HPC cluster

About the CLARA project

High-performance computing system CLARA@UNIBA.SK (CLustered Academic Research Appliance) is one of the latest additions to the portfolio of services of the Centre of Information Technologies (CIT CU). It is provided in the  SAaOS form (Software As an Optimised Service) since January 15, 2020, for research teams across the Comenius University. The cluster is prepared for theoretical-chemical and theoretical-physical computing, utilizing massive parallelized matrix operations, often used in chemistry, pharmacy and biology.

The CLARA system consists of interconnected clustered computing nodes, system and application package. It was implemented, configured and optimized for permanent high load operation and computing power by professionals at CIT CU in late 2019. With its relatively low energy consumption, CLARA also meets the standards of green computing.

Basic technical information - CLARA@UK

ManufacturerSupermicro
HardwareSYSF619P2-RT/ X11DPFR
CPU type2xCPU – Intel Xeon Silver 4216
CPU parameters2.1GHz, 16C/32T, AVX-512 FMA
Interconnectivity56G InfiniBand + 2x10G Ethernet
Number of modules
(dimensional factor 4U)
1
Number of computing nodes 8
Number of CPU sockets16
Number of interconnecting devices InfiniBand 1
Current configuration round-up256 cCPU, RAM 2,5TB, SDD 38TB
Current installed computing power for Double Precision aritmethic8 TFLOPS
Current energy consumption<2kW
Installed system softwareCentOS 7.4, Sun Grid Engine SGE v.8.1, Open MPI v.2.1, gcc / gfortran  v.4.8
Optimized mathematical librariesOpenBLAS v.0.3.8, ATLAS v.3.10.3 LAPACK v.3.9.0

Key quantitative usage parameters - March 15, 2020

Parameter Value Units
users total 32 researchers
number of finished tasks 4622 pcs
average task duration 13325 seconds
"virtual" CPU** time total 4637 days
number of I/O operations (read/write bytes) 40,7 PB
**=reduction to 1 physical core, how long would the computing process take    
APPLICATIONS
Number of tasks %
DIRAC 637 14
GAUSSIAN 2576 56
Open MOLCAS 1200 26
NWCHEM 32 1
SCHRODINGER 177 4
CFOUR    
GROMACS    
MRCC    

Research projects with top usage of computing resources CLARA@UK

Lead researcher: Doc. Pavel Neogrády, DrSc.

Research project: Referenčné výpočty vlastností, interakcií a reaktivity chemických systémov.

Field of research: Theoretical and Computational Chemistry


Lead researcher: Prof. Ivan Černušák, DrSc.

Research project: Eurofusion WPHCD-2020-ENR Computational modelling of Cs-Mo and impurities interactions in NBI sources                                          

Field of research: Materials chemistry / Dissertation - Mgr. Silvia Kozáková


Lead researcher: Prof. Ivan Černušák, DrSc. a Dr. Florent Louis (Univ. Lille)

Research project: Chemical reactivity of halogens in troposphere (bilateral cooperation CU and UL)

Field of research: Atmospheric Chemistry


Lead researcher: Florent Louis (Associate Professor)
Participants : Florent Louis (Associate Professor), Sonia Taamalli (Research Engineer), Zainab Srour (Master 2 student in Atmospheric Environment)
Address : PhysicoChimie des Processus de Combustion et de l’Atmosphère (PC2A), UMR CNRS/Université de Lille 8522, Université de Lille, Bât. C11, 59655 Villeneuve d’Ascq, France

Research project: Atmospheric chemistry of halogenated species

Field of research: Computational Chemistry 


Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.

Research project: APVV-17-0239 Computer-aided design, synthesis, activity-testing and disposition of inhibitors of neuraminidases of influenza A virus as potential antiviral compounds

Field of research: Molecular Modeling and Antimicrobial Agent Design


Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.

Research project: VEGA 1/0228/17 Research of antimicrobial compounds and their effects on model cellular membranes

Field of research: Molecular Modeling and Anti-viral Agent Design


Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.

Research project: Modeling of structure-function relationships of mutant proteins of patients with genetic degeneration of retina

Field of research: Rigorous thesis, Mgr. Adam Hotra, PhD.


Lead researcher:   Doc. Ing. Vladimir Frecer, DrSc.

Research project: QSAR and research of antimicrobial peptidomimetics

Field of research: Rigorous thesis, Mgr. Peter Polonec


Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.

Research project: QSAR and design of new antiviral compounds

Field of research: Master's theses Michal Talapka


Lead researcher: RNDr. Lukas Felix Pasteka PhD.

Research project: Theoretical spectroscopy of selected molecules and their suitability for laser

Field of research: Dissertation, Andrej Hurajt


Lead researcher: prof. RNDr. Miroslav Urban, DrSc.

Research project: CCSD(T) benchmarks for DFT modeling of covalent and dispersion interactions in polyethylene cross-linked by metal atoms

Field of research: Materials Chemistry


Lead researcher: Radovan Šebesta; other researchers: Mgr. Patrícia Čmelová (doctoral student)

Research project: Hybrid peptide – tiourea catalysts (topic within project APVV-18-0242, Asymmetric multicatalysis for effective synthesis of chiral carbocyclic and heterocyclic compounds)

Field of research: Organic chemistry (asymmetric calatysis)


Lead researcher: Radovan Šebesta; other researchers: Mgr. Dominika Krištofíková (doctoral student)

Research project: Stereoselective domino reactions with mechanical activation (topic within project VEGA 1/0332/19, Mechanochemistry – a tool for effective asymmetric catalysis)

Field of research: Organic chemistry (asymmetric calatysis)

Extent of utilization of cluster resources - 24 hours